[PRE REVIEW]: pyPLNmodels: A Python package to analyse multivariate high-dimensional count data #6965

editorialbot · 2024-07-07T04:25:46Z

Submitting author: @Bastien-mva (Bastien Batardiere)
Repository: https://github.com/PLN-team/pyPLNmodels.git
Branch with paper.md (empty if default branch): joss
Version: 0.0.78
Editor: @likeajumprope
Reviewers: @LingfengLuo0510, @mrazomej
Managing EiC: Chris Vernon

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/1f6f471f36670700a9d70ccd03654038"><img src="https://joss.theoj.org/papers/1f6f471f36670700a9d70ccd03654038/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1f6f471f36670700a9d70ccd03654038/status.svg)](https://joss.theoj.org/papers/1f6f471f36670700a9d70ccd03654038)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-07-07T04:25:49Z

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editorialbot · 2024-07-07T04:26:06Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (705.1 files/s, 171888.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1380           3087           6043
CSV                             10              0              0           1948
Markdown                         3             87              0            360
R                                2             30              9            171
TeX                              1             12              0             83
YAML                             2              8             17             79
Jupyter Notebook                 1              0           1026             64
TOML                             1              6              8             53
DOS Batch                        1              8              1             26
reStructuredText                 7             13             56             17
Bourne Shell                     1              2              0             13
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1550           4211           8866
-------------------------------------------------------------------------------

Commit count by author:

   631	bastien-mva
    11	Julien Chiquet
     9	Jean-Benoist Leger
     1	Joon Kwon

editorialbot · 2024-07-07T04:26:10Z

Paper file info:

📄 Wordcount for paper.md is 1747

✅ The paper includes a Statement of need section

editorialbot · 2024-07-07T04:26:11Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot · 2024-07-07T04:26:14Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fevo.2021.588292 is OK
- 10.5281/zenodo.5765804 is OK
- 10.1093/biomet/76.4.643 is OK

MISSING DOIs

- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- 10.25080/majora-92bf1922-011 may be a valid DOI for title: statsmodels: Econometric and statistical modeling ...
- 10.1214/18-aoas1177 may be a valid DOI for title: Variational inference for probabilistic Poisson PC...
- No DOI given, and none found for title: gllvm - Fast analysis of multivariate abundance da...
- No DOI given, and none found for title: Zero-inflation in the Multivariate Poisson Lognorm...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package

INVALID DOIs

- None

editorialbot · 2024-07-07T04:27:03Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-07-07T04:27:50Z

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Bastien-mva · 2024-07-07T10:10:16Z

@editorialbot commands

editorialbot · 2024-07-07T10:10:17Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Bastien-mva · 2024-07-07T10:10:41Z

@editorialbot commands

editorialbot · 2024-07-07T10:10:44Z

Hello @Bastien-mva, here are the things you can ask me to do:


# List all available commands
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Bastien-mva · 2024-07-07T10:11:17Z

@editorialbot check repository

editorialbot · 2024-07-07T10:11:35Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (700.4 files/s, 169699.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1380           3087           6043
CSV                             10              0              0           1948
Markdown                         3             67              0            290
R                                2             30              9            171
TeX                              1             12              0             83
YAML                             2              8             17             79
Jupyter Notebook                 1              0           1026             64
TOML                             1              6              8             53
DOS Batch                        1              8              1             26
reStructuredText                 7             13             56             17
Bourne Shell                     1              2              0             13
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1530           4211           8796
-------------------------------------------------------------------------------

Commit count by author:

   632	bastien-mva
    11	Julien Chiquet
     9	Jean-Benoist Leger
     1	Joon Kwon

editorialbot · 2024-07-07T10:11:39Z

Paper file info:

📄 Wordcount for paper.md is 1106

✅ The paper includes a Statement of need section

editorialbot · 2024-07-07T10:11:40Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

Bastien-mva · 2024-07-07T10:45:16Z

At-mentioning co-authors here: @jchiquet @joon-kwon

Here is a non-exhaustive list of potential reviewers from the JOSS reviewers google sheet (coauthors, please feel free to add more in this thread):

richford
ZhenchenHong
LingfengLuo0510
mayer79
mrazomej
DanWaxman
simeonhebrew
matt-graham
roualdes
prdm0
Wrzlprmft
misken
vankesteren
limengbinggz
larryshamalama
nickelnine37
zhenmuw.edu
janfb
papachristoumarios
edrictam
maximtrp
Rlucas7
tylerwmarrs

Bastien-mva · 2024-07-07T11:04:07Z

@editorialbot check repository

editorialbot · 2024-07-07T11:04:25Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (703.7 files/s, 170455.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1380           3087           6043
CSV                             10              0              0           1948
Markdown                         3             65              0            289
R                                2             30              9            171
TeX                              1             12              0             83
YAML                             2              8             17             79
Jupyter Notebook                 1              0           1026             64
TOML                             1              6              8             53
DOS Batch                        1              8              1             26
reStructuredText                 7             13             56             17
Bourne Shell                     1              2              0             13
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1528           4211           8795
-------------------------------------------------------------------------------

Commit count by author:

   633	bastien-mva
    11	Julien Chiquet
     9	Jean-Benoist Leger
     1	Joon Kwon

editorialbot · 2024-07-07T11:04:29Z

Paper file info:

📄 Wordcount for paper.md is 1092

✅ The paper includes a Statement of need section

editorialbot · 2024-07-07T11:04:30Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

Bastien-mva · 2024-07-07T11:15:06Z

@editorialbot check repository

editorialbot · 2024-07-07T11:15:30Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (700.1 files/s, 169563.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1380           3087           6043
CSV                             10              0              0           1948
Markdown                         3             65              0            288
R                                2             30              9            171
TeX                              1             12              0             83
YAML                             2              8             17             79
Jupyter Notebook                 1              0           1026             64
TOML                             1              6              8             53
DOS Batch                        1              8              1             26
reStructuredText                 7             13             56             17
Bourne Shell                     1              2              0             13
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1528           4211           8794
-------------------------------------------------------------------------------

Commit count by author:

   634	bastien-mva
    11	Julien Chiquet
     9	Jean-Benoist Leger
     1	Joon Kwon

editorialbot · 2024-07-07T11:15:35Z

Paper file info:

📄 Wordcount for paper.md is 1070

✅ The paper includes a Statement of need section

editorialbot · 2024-07-07T11:15:37Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

Bastien-mva · 2024-07-07T11:17:54Z

@editorialbot check references

editorialbot · 2024-07-07T11:18:17Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fevo.2021.588292 is OK
- 10.5281/zenodo.5765804 is OK
- 10.1093/biomet/76.4.643 is OK

MISSING DOIs

- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- 10.25080/majora-92bf1922-011 may be a valid DOI for title: statsmodels: Econometric and statistical modeling ...
- 10.1214/18-aoas1177 may be a valid DOI for title: Variational inference for probabilistic Poisson PC...
- No DOI given, and none found for title: gllvm - Fast analysis of multivariate abundance da...
- No DOI given, and none found for title: Zero-inflation in the Multivariate Poisson Lognorm...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package

INVALID DOIs

- None

Bastien-mva · 2024-07-07T11:27:36Z

@editorialbot check references

editorialbot · 2024-07-07T11:27:56Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fevo.2021.588292 is OK
- 10.25080/majora-92bf1922-011 is OK
- 10.5281/zenodo.5765804 is OK
- 10.1093/biomet/76.4.643 is OK
- 10.1214/18-aoas1177 is OK

MISSING DOIs

- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: gllvm - Fast analysis of multivariate abundance da...
- No DOI given, and none found for title: Zero-inflation in the Multivariate Poisson Lognorm...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package

INVALID DOIs

- None

crvernon · 2024-07-08T14:10:11Z

@editorialbot invite @likeajumprope as editor

👋 @likeajumprope - do you want to take this one on as editor?

editorialbot · 2024-07-08T14:10:14Z

Invitation to edit this submission sent!

likeajumprope · 2024-07-08T14:11:54Z

Invitation to edit this submission sent!

sure!

likeajumprope · 2024-07-08T14:12:43Z

@editorialbot assign @likeajumprope as editor

editorialbot · 2024-07-08T14:12:45Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

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likeajumprope · 2024-07-08T14:14:05Z

@editorialbot commands

editorialbot · 2024-07-08T14:14:07Z

Hello @likeajumprope, here are the things you can ask me to do:


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likeajumprope · 2024-07-08T14:14:40Z

@editorialbot assign @likeajumprope as editor

editorialbot · 2024-07-08T14:14:42Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

likeajumprope · 2024-07-08T14:15:32Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

what am I doing wrong haha
can you assign me @crvernon?

crvernon · 2024-07-08T14:22:19Z

@editorialbot assign @likeajumprope as editor

I believe only editors in chief can run assignments on a name (even if it is your own). You have to actually run:

@editorialbot assign me as editor

No problem though, I've got you on this one. And thanks!

editorialbot · 2024-07-08T14:22:23Z

Assigned! @likeajumprope is now the editor

likeajumprope · 2024-07-09T17:21:01Z

Hi @LingfengLuo0510 👋 - would you be interested in taking on this paper for review?

likeajumprope · 2024-07-09T17:22:44Z

Hi @mayer79 👋 would you be interested in taking on this paper for review?

likeajumprope · 2024-07-09T17:24:16Z

Hi @mrazomej 👋 would you be interested in taking this paper on for review?

LingfengLuo0510 · 2024-07-09T17:26:09Z

Hi @LingfengLuo0510 👋 - would you be interested in taking on this paper for review?

Thanks! Yes I am interested.

likeajumprope · 2024-07-09T17:27:31Z

Hi @LingfengLuo0510 👋 - would you be interested in taking on this paper for review?

Thanks! Yes I am interested.

perfect thanks!!

likeajumprope · 2024-07-09T17:28:30Z

@editorialbot add @LingfengLuo0510 as reviewer

editorialbot · 2024-07-09T17:28:33Z

@LingfengLuo0510 added to the reviewers list!

mrazomej · 2024-07-09T17:36:16Z

Hi @mrazomej 👋 would you be interested in taking this paper on for review?

Yes, I'm interested. Count me in!

likeajumprope · 2024-07-09T17:38:48Z

@editorialbot add @mrazomej as reviewer

likeajumprope · 2024-07-09T17:40:14Z

@editorialbot add @mrazomej as reviewer

editorialbot · 2024-07-09T17:40:16Z

@mrazomej added to the reviewers list!

likeajumprope · 2024-07-09T17:40:54Z

Thanks heaps @mrazomej and @LingfengLuo0510! I will then start the review process!

likeajumprope · 2024-07-09T17:41:11Z

@editorialbot start review

editorialbot · 2024-07-09T17:41:14Z

OK, I've started the review over in #6969.

editorialbot added pre-review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Jul 7, 2024

editorialbot assigned likeajumprope Jul 8, 2024

editorialbot assigned LingfengLuo0510 Jul 9, 2024

editorialbot assigned mrazomej Jul 9, 2024

editorialbot closed this as completed Jul 9, 2024

[PRE REVIEW]: pyPLNmodels: A Python package to analyse multivariate high-dimensional count data #6965

[PRE REVIEW]: pyPLNmodels: A Python package to analyse multivariate high-dimensional count data #6965

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